KDM5B p.Val307=
c.921G>C · rs2527565593 · VCV3032252
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.9e-05%)
Conditions
1
KDM5B-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.56 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -3.7, phastCons 0.3 |
| Overall | ||
| CADD | 11.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.9e-05%
Overall
6.9e-05%
1/1,450,102 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- KDM5B
- Protein
- p.Val307=
- Coding
- c.921G>C
- MANE Select
- NM_006618
- dbSNP
- rs2527565593
- Type
- single nucleotide variant
- Location
- chr1:202760571 (GRCh38)
- Gene constraint
- LOEUF 0.858 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.52 · 56 PDB
- Residue 307
- a UniProt-annotated variant site (in mrt65)
Disease context
KDM5B-related disorder
Similar variants
- KDM5B p.Arg1214Ter Likely pathogenic ★★ same condition
- KDM5B p.Arg1253Ter Pathogenic/Likely pathogenic ★★ same condition
- KDM5B c.4022-1G>C Likely pathogenic ★ same condition
- KDM5B p.Gln1182Ter Likely pathogenic ★ same condition
- KDM5B p.Ser1312Ter Likely pathogenic ★ same condition
- KDM5B p.Pro163Leu Uncertain significance ★ ⚠ same condition
- KDM5B p.Gln106Ter Likely pathogenic same condition
- KDM5B c.204+5G>T Uncertain significance same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/kdm5b-p-val307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown